This paper proposes a method to reduce the limit cycle phenomenon that appears in the steady-state response of a pendubot system, when it is controlled by a state feedback controller based on the linearized system model. For this, we employed the compensator which estimates the friction based on the LuGre model in the LQR control. The proposed compensation method is validated by experiments for a pendubot system, which shows that the external disturbance as well can be efficiently compensated.